I'm enjoying Darksiders, and I'm definitely understanding why some folks compare it to Legend of Zelda.

In Zelda, you can fill up your bottles with Milk, Potion, or Fairies, and in Darksiders, it appears you're able to do the same with your Empty Vessels (though less Milk and more Souls, probably). However, I've yet to actually find out how to do so. The Empty Vessels can't be used directly (like one might equip a bottle in a Zelda game) so I'm at a bit of a loss.

How can you fill an Empty Vessel with Revive, Life Essence, Wrath, or Chaos (etc)?

In my experience, the game's checkpoint system is forgiving enough that I never really needed to use my vessels. If you're going for achievements/trophies, you should save your souls for maxing your weapons. In Zelda, you get to a point where you basically have more money than you will ever spend, but that doesn't happen in Darksiders. (Maybe it would if you played through a second time on Apocalyptic difficulty?)